• Theoretically Speaking by Mike Fowler

    I'll use this forum to post my ideas about work I'm doing, work I've read, or things that pop into my head; hopefully to raise discussion and help me learn more about this crazy little thing called science.

    • La Vida Loca

      Wednesday, 04 Nov 2009

      Well folks, this is it. Chapter the newth.

      I’ve taken the plunge and entered Mediterranean life. A new position in a new Institute in a new country. Same old continent though. After 7 years in Helsinki, you can’t ask for too much.

      I’m continuing my ongoing education at the Institut Mediterrani d’Estudis Avançats. I started here this week, after a month of hectic tying up loose ends, including the successful defence of my 1st PhD student’s thesis on Ecological communities in variable environments: dynamics and diversity under coloured environmental stochasticity


      Some colours, stochasticing, earlier this eon.

      Congratulations, Lasse. It was an excellent piece of science, and an absolute pleasure working on this with you.

      So now, to pastures new. I moved into my new office on Monday, the 2nd of November, 2009.


      A steep pasture, newly, yesterday.
      From the new desk.

      I’ve joined the Seabird Ecology Group, in Mallorca, where I shall be working more on coloured noise (temporally correlated stochastic variation), metacommunities (spatially structured interspecific assemblages) and integrating theory with data collected from seabird populations. My new group have particular expertise in seabird demography, focusing on species of local conservation importance (e.g., Cory’s shearwater, Audouin’s gull, Balearic shearwater), branching out into reptiles and mammals if and when possible.

      I just hope the gulls can count properly, no matter how endangered they think they are. They’ll be even more endangered if they don’t behave according to the theory…

      Something I’ve been meaning to do on this blog is try to communicate important ideas from mathematical biology to a non-specialist audience. I’ve so far singularly failed to do that. I find it’s hard enough writing for other theoreticians, never mind other ecologists. Hopefully this will change in the near future, and with the help and encouragement of my new group.

      Fins d’ara, i que vagi molt bé!

    • Am I doing something right, or wrong here?

      Friday, 25 Sep 2009

      Just back from a trip to Mallorca; for business, rather than pleasure, you understand1. I’m moving to a new position in the Population Ecology Group at IMEDEA, the Mediterranean Institute for Advanced Studies, starting in November.

      These, then, are busy times. Having to sell a house in Finland, and figure out what to do with the contents; find a new house in a new country, and figure out how to fill that up; trying to finish up as many projects in Finland as possible, so I can hit the ground running and (crucially) looking forward when I touch down in Mallorca; travelling back, forward, up, down and sideways; the list goes on.

      So why, oh why, is my inbox rapidly filling up with requests to review manuscripts? At the last count, I reckon I’ve had eight in the last month. I accepted the first one, not knowing quite what was in store, but simply haven’t had time to accept any others. Apologies to those Eds and authors who’ve had to find alternatives and the delay this causes (in fact, one journal already found an alternative before I’d even managed to respond to their initial request – that’s an excellently run review system).

      So what have I done to deserve this attention? How do they know that I’m rushing about like a blue ersed fly at the moment?

      Is it because I usually make every effort to return my reviews within the requested time limits? Because I actually attempt to write more than three lines in response to the efforts the authors have made, or read up on concepts I don’t quite understand, rather than dismissing them before writing the review? (Did I pack that old high school maths textbook already?). Is it my sour, churlish particularly honest reviewing style that Editors find so appealing?

      Or is it because I’ve been sending out piles of tedious drivel to these same journals over the last few years and the Eds just want to give me a taste of my own medicine? Answers on the back of a self-addressed postcard, please.

      Now that’s out of my system, I’d better get back to finishing that first review. I think it was due yesterday.

      Then I have to find and pack my new school uniform, specially designed for the Mediterranean climate.


      I say, the crabs are bit feisty this morning

      1 Although it certainly was a pleasure doing business over there.

    • Paying to support Open Access.

      Wednesday, 09 Sep 2009

      Open Access is often a topic that raises vociferous discussion on NN. After arriving back from a relaxing tour of the Roman remains around the Lazio region of Italy, having drunk my fill of Barolo, I was pleased to finally get round to checking out some of the TOCs festering away in my Inbox this morning.

      PLoS Biology have an interesting article that doesn’t seem to have been picked up on NN yet, so I thought I’d point it out to interested readers.

      Stuart Shieber has published an article which highlights an inequity between subscription and Open Access journal models1.

      He did a good job of grabbing my attention with the following controversial statement:

      the subscription-fee business model has manifested systemic dysfunctionalities in practice.

      Ooooh – mystery, intrigue and a delightful dollop of dysfunctionality. What could the scandal be? I’ll return to that later.

      As we get into the article, Shieber outlines his basic problem with how authors face up to the decision of submitting their article to traditional (subscription based) versus processing-fee (Open Access, where the author pays a fee to cover publication costs if the article is accepted) journal models.

      The problem is, of course, that the [e.g.] US$1,500 article revenue to the journal that is provided by the processing fee under the processing-fee model is hidden in subscription charges in the subscription-fee model, and these are typically paid not by the authors, even in their role as readers of the journals, but on their behalf by subscribing research institutions, typically university research libraries. The authors don’t see these charges; hence, they don’t enter their economic calculus. Yet authors are now expected to pay these charges under the open-access processing-fee model. It is no wonder they might be expected to submit preferentially to closed-access journals. Indeed, it is a wonder that authors, even now, are willing to submit to processing-fee-charging open-access journals.

      Shieber goes on to outline a proposal that would encourage Universities and Funding Agencies to set aside non-fungible (i.e., non-interchangable) sources of cash to pay for both traditional subscriptions and processing-fees. He highlights that the Wellcome Trust is already running such a scheme, and other universities in Europe and North America have established funds to assist with processing-fees. Good on them!

      Shieber adds some caveats and issues surrounding implementation of such schemes, with another potential controversy arising from his statement that funding bodies and/or researchers have an

      underlying goal of providing a sustainable mechanism for supporting open-access journals.

      The controversy?

      • Why should we financially support open-access journals?

      Well, the obvious retort that springs to my mind is “Why should we publicly support privately owned subscription based journals?”. I guess the underlying insinuation is that we should support Open Access, as it has the potential to disseminate our publicly funded research further.

      Shieber then gets into the juicy stuff, which unfortunately isn’t quite so juicy. A brief discussion of how hybrid systems (e.g., Springer’s Open Choice) that are currently in place could lead to a “tragedy of the commons”, as the impact of authors paying to publish is diluted across all subscription payers, leading to incredibly minor reductions in subscription fees across all Universities. This is overcome by excluding such hybrid journals from the OA pot.

      One problem I have with this otherwise interesting article and concept is the discussion of “caps” by funders and universities, based on a “typical” author publication rate, with authors then trading off between submitting to OA with author fee and subscription with libraries covering the cost.

      I believe Universities are institutions that should help and encourage the most academically gifted individuals, rather than reduce standards to a lower common denominator. I think some of Shieber’s arguments start to unravel a bit here. By basing his trade-off scheme on a “cap” calculated as a percentage of the grant acquired by a researcher, he seemingly overlooks the fact that different research fields typically require and gain different amounts of funding.

      I’m cheap baby – as a theoretician and modeller, my main research costs are my drinking salary. Even my shiny new computer was a snip, costing easily less than a month’s salary. I don’t do any lab work, so no expensive machines or reagents to include in my grant applications. I don’t do field work, so no equipment to buy for that either. Although rubber boots are often cheaper than a computer.


      A handy mobile phone holder

      So, under Shieber’s proposal, I would be more limited in my choice of where to submit articles than someone who has more expensive research costs. There’s likely to be huge variation within and between fields, which will impact upon who gets to submit where, which can then feedback to who is successful in future grant applications. This is a tricky point to overcome.

      I enjoyed this article. It was Open Access, and agreed with many of my opinions about publication models, so not much surprise that I like it. By specifically shifting some public money specifically towards OA (processing-fee) journals, Shieber argues, we actually make the publishing system fairer and more competitive. This should eventually curb the hyperinflation of subscription fees that is currently reducing access to all journal articles, and could present a “cost neutral” solution to switching form one dominant publication model to a more balanced situation.

      But, by supporting OA in this way, is there a danger of unfairly squeezing some journals out of the market? I’m not convinced of this – we’ve been supporting for profit publishing houses with public money for some time now. If they can’t face up to balanced competition, they shouldn’t be there. If there’s a niche in the market for a certain type of journal, the most appropriate model should be able to occupy it.

      It doesn’t make all that much sense to continue with a certain approach just because it’s the status quo. But, I like it, I like it, I la-la-la-like it it’ll be interesting to see if Shieber’s arguments start to affect policy soon.

      1 Shieber SM (2009) Equity for Open-Access Journal Publishing. PLoS Biol 7(8): e1000165. doi:10.1371/journal.pbio.1000165

    • Evolution of a new life-form?

      Thursday, 27 Aug 2009

      The Strandbeesten.

      I don’t know where it came from, I don’t really know what it is, but I know I want one.

      STRANDBEESTEN_TRAILER from Alexander Schlichter on Vimeo.

      The video is wonderfully wistful, which adds somewhat to my melancholy. We just sold our apartment this afternoon1. My time in Finland is drawing to an end.

      1 And ‘Anchor Me’, by the Mutton Birds is playing on my digital music machine as I write this. More melancholy…

    • Say "Hebbo" to Tarvuism

      Thursday, 13 Aug 2009

      It’s been a while since I had anything to say on the blogs; summer, work, spending time in the Theoretical Population Dynamics Forum, etc.

      So, to maintain some sort of presence here, I invite you all to say “Hebbo” to Tarvuism.

      Really, it’s so easy.

      Say Hebbo! from Torvakian on Vimeo.

      http://www.tarvu.com/

      Learn how to speak to cephalopods


      That’s pronounced spblubblaplub

    • Finland is catching up with the more westerly parts of Europe.


      Translate this, if you dare risk eternal, fiery damnation

      Finnish news agency YLE, reports that complaints are filing in against the popular atheist humanist thoughtful persons bus ads that are appearing over here. Filing in two by two, I hope. Well, no. They’ve only received one so far.

      I love the unequivocal quote from YLE website

      According to the complaint, the cheery ad campaign for atheism is slanderous and breaches UN human rights treaties.

      Far from being slanderous, it’s downright cheery!

      Next week, I hope to report on the Finnish response to the local release of the latest 7-inch popular music disc from upcoming beat quartet, The Beatles.

      Now, if I’m quick enough, I might even get two blog posts in a row!

    • A rose by any other name

      Monday, 29 Jun 2009

      Impact factors again, folks. Plenty of discussion about those and other indices of our personal scientific worth, just search for the impact factor tag on NN for e-sheaths and screeds of disgruntlement, or see here for a more gladiatorial point of view.

      I shall merely take the opportunity today to present some simple stats about those simple stats.

      I took the top 60 journals in Ecology and Evolutionary Biology (ranked by 2-year Impact Factor) from the ISI Journal Citation Reports for 2008. I looked at 6 of the statistics published by ISI based on different :

      • Impact Factor (2-years)
      • 5-Year Impact Factor
      • Immediacy Index
      • Cited Half-Life (adjusted so anything ≥ 10 was set to 10)
      • EigenfactorTM Score
      • Article InfluenceTM Score

      I calculated Pearson’s linear correlation coefficient for those scores across 57 of the top 60 journals (3 were excluded, lacking 5-year IF and Article Influence scores0).

      And here are the results:

      Table 1. Correlation between different indices on ISI Journal Citation Reports_1
      !http://farm4.static.flickr.com/3403/3671403588
      470c0ed892.jpg?v=0!

      So, what can we take from this? Well, I was interested in how similar these metrics were, in terms of describing, urrrr, anything about the journals and/or their content. Basically, there are a few different options to choose from; do they actually tell us different things, or do they all say pretty much the same?

      Well, it seems that 2- and 5-year Impact Factor tell us a pretty similar story (r0 = 0.712). A journal with a high (or low) 2-year IF will generally also have a high (low) 5-year IF. This is probably to be expected as the same information is used for both metrics (2 years is a subset of 5 years).

      EigenfactorTM seems to give us slightly different information2, and Half-life is generally unrelated to any other index across these journals. These last two indices hopefully give us novel information about journals and their content.

      One result sprang out for me. The 5-year IF and Article InfluenceTM appear to tell us almost exactly the same thing (r0 = 0.983!).


      Figure ∆: Spot the difference.

      So, do we really need all these different metrics? The above analysis is quick and dirty, to say the least. I haven’t even gone into what the different metrics actually mean here. But with concerns about how IF is used to judge individual scientists, and new metrics springing up reasonably often, it’s worth asking how useful the new metrics really are. How much extra information can be gleaned while having to differentiate between what the new indices really mean and their method of calculation?

      Article influence can potentially be dumped at the journal level – it just duplicates 5-year IF information. But if it tells us something about individual papers, then it retains utility.

      In fact, Article Influence is a measure of the per-article influence of a given journal, which is the Eigenfactor scaled by something called the “normalised article vector”. As far as I can tell, this vector relates to the number of articles a journal publishes, so AI is the Eigenvalue scaled to be comparable to Impact Factor.

      This tells us that the normalised article vector does something important to the Eigenfactor, as EF and IF (2- or 5) don’t correlate too strongly. So, Article Influence really doesn’t add anything new to the story, and Eigenfactor is just a longer term impact factor, lacking information about the number of articles a journal actually publishes. There’s been a bit of hope about what these new measures can offer, but I’m not yet convinced these two actually add anything new or more intuitive to the story.

      Now I just need to think of a snappy way to end this post. I have the same problem finishing off my Discussions in manuscripts.

      Snap.


      0 These were ranks 35 (Biogeosciences), 47 (Biol. Invas.) and 55 (J. Syst. Paleontol.)

      1 How on earth do you make tables on NN? This ‘table’ is a screen shot from a word processing document.

      2 Duncan, if you’re reading this, my analysis of Eigenfactor sort of goes against the view in your blog post. Different set of journals? Any comment?

    • Test driving Zotero

      Thursday, 18 Jun 2009

      I’m a Mac user, and over the last few years, I’ve wanted to move away from using proprietary software wherever possible. This basically means exchanging MS Word/Excel for OpenOffice, switching my simulation and analysis software Matlab for R, my time wasting literature searching and blogging activities from Safari to Firefox and my reference software Endnote for some freeware alternative.

      Unfortunately, Endnote hasn’t had good support for OpenOffice on Mac to date, so I’ve been searching for alternatives that are as flexible across environments and operating system versions as possible, to allow me to make the switch as seamlessly as possible. I have different versions of Mac OSX’s on my laptop and desktop machines, with all sorts of jumbles of software versions and licences meaning I’m a tough customer when it comes to compatibility issues.

      So, is Zotero the answer to my long suffering frustrations? The best way to describe it comes from their own website:

      Zotero [zoh-TAIR-oh] is a free, easy-to-use Firefox extension to help you collect, manage, and cite your research sources.

      Martin Fenner has written a couple of posts about reference manager software options here and here, and interviewed Trevor Owens from Zotero so I’d like to take this opportunity to state that I’ve spent the last couple of days road testing Zotero as follows:

      • on different machines (PPC and Intel Macs),
      • running different versions of the operating system (OSX.4, OSX.5),
      • different versions of Zotero (Zotero v.1 on the PPC OSX.4, Zotero v.2 on the Intel OSX.5)
      • different word processors (OpenOffice v.2.4, Word 2004 & 2008)


      Good boy! Zotero sits nicely in the bottom of your foxy web browser.

      and so far, I’m reasonably happy with it’s within species performance. Installing the required plugin for Citation capability in OpenOffice was a bit sticky, but it seems to work nicely now.

      Importing my reference library from Endnote was straightforward1. Once imported, I basically want to use my reference manager to stick in article citations when I’m writing a manuscript and generate a bibliography at the end of the paper.

      Insertion of the citations is done easily in Zotero, and produces a lovely bibliography at the end. There are only a few output styles included in the basic Zotero download, but others are easily available, if a little tedious to install – they seem to need to be installed individually.


      Endnote begone! I will switch my CWYW allegiances to Zotero!

      Zotero also easily finds and incorporates citation information from webpages into your own database, e.g., downloading citation information from a doi accessed webpage, simply by clicking an icon in the address bar.

      The major problem I’ve found so far is backwards compatibility. It doesn’t manage to switch the same document between different versions of Word (2004 vs. 2008), due to the different versions of Zotero required for older and newer Word versions (v.1 for 2004; v.2 for 2008). Documents are viewable, but citations are not editable.

      Moving from OpenOffice (2.4 on the PPC) to Word 2004/8 wasn’t possible. This seems to be a problem with OpenOffice’s ability to save the documents in a sufficiently recent Word version (the most recent offered was Word ‘97/2000/XP), and Word’s inability to read and convert *.odt documents.

      One further potential downside for avid Mac users is that Zotero only has limited compatibility with Pages 2 and for all users, limited compatibility with Google docs. Drag and drop bibliography lists are allowed, but I haven’t found out how to Cite while you Write in these environments yet. These are projects I hope Zotero are already tackling, but they’re doing a reasonably good job so far.

      There are more features I haven’t even begun to explore yet, such as storing your reference database online for easy switching between computers and sharing info with collaborators. This last option will be useful to me as my tame PhD. student has just moved to Canada, and we still have joint projects to work on.

      In conclusion, I like Zotero. It’s intuitive, does exactly what I want it to do within my manuscripts, works well with OpenOffice, but needs a bit of work for moving between systems, which will be important for the collaborative claims made with online functions. But most of all, it’s good cos it’s FREE!

      1 Export as a Bibtex library (Endnote 9) or RIS format (Endnote X2).

      2 Even though Pages is proprietary software, I have a copy installed, but I try to avoid using it where possible. Google docs functionality would be much more appreciated.

    • What's all the twittering fuss about?

      Tuesday, 09 Jun 2009

      Although I have tentatively embraced (very British of me) the macro-weblogging world, I am pleased to say that I shun other faddish forms of frivolous webfrippery.

      The bastion of all news sources, Auntie Beeb, reports that (much like jaded ol’ capitalism), 90% of twitter tweets are posted by 10% of sad loners tweeting twits.

      Try saying that after a facefull of Tia Maria’s!

      Harvard business school researchers went on to say:

      And most people only ever “tweet” once during their lifetime.

      I find it hard enough to maintain regularly activity on this blog (although I theoretically hang about here a bit more often), never mind micro-blogging mundane minutes more metronomically.

      In other news, it’s Mrs F’s birthday today. Feliç aniversari, hotlips!

      I’m now going to one-up Bob and go for a wireless walk, without my laptop.


      Not Mrs F. Some fictional time ago.

      That is all.

    • Space, the final frontier

      Wednesday, 20 May 2009

      I went to see the old new Star Trek film last week. And knock me down with a feather, but it was fantastic1. I recommend going to check it out if you get the chance. Rip roaring fun, with plenty of nods and winks for fans of the original Roddenberry Star Trek series.

      But the point of this post is not about fantasy. Rather, the reality of humans actually travelling to space. The European Space Agency is announcing its latest batch of recruits today, at 13.00 local time (CET).

      They will stream a live press conference online here, and a colleague of mine is down to the final group for selection, after an initial 10,000+ applied.

      Jussi, good luck to you! I genuinely hope you make it, so you can send us a postcard from Alpha Centauri!

      1 Except Simon Pegg’s dodgy Scottish accent. It was almost passable, but for some reason he confused the personal pronoun “I” with the exclamation often uttered after blunt force is applied to a testicle “Aaaaiiieeeee!”


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